Mark DePristo aaf11f00e3 Near final BCF2 implementation ... -- Trivial import changes in some walkers -- SelectVariants has a new hidden mode to fully decode a VCF file -- DepthPerAlleleBySample (AD) changed to have not UNBOUNDED by A type, which is actually the right type -- GenotypeLikelihoods now implements List<Double> for convenience. The PL duality here is going to be removed in a subsequent commit -- BugFixes in BCF2Writer. Proper handling of padding. Bugfix for nFields for a field -- padAllele function in VariantContextUtils -- Much better tests for VariantContextTestProvider, including loading parts of dbSNP 135 and the Phase II 1000G call set with genotypes to test encoding / decoding of fields.		2012-05-24 10:57:02 -04:00
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writer	Near final BCF2 implementation	2012-05-24 10:57:02 -04:00
AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	Near final BCF2 implementation	2012-05-24 10:57:02 -04:00
GenotypeUnitTest.java	Change interface to getNegLog10PError to getLog10PError	2011-11-18 21:07:30 -05:00
GenotypesContextUnitTest.java	GenotypesContext now updates cached data for add, set, replace operations when possible	2011-11-22 08:40:48 -05:00
VCFJarClassLoadingUnitTest.java	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -04:00
VariantContextBenchmark.java	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
VariantContextTestProvider.java	Near final BCF2 implementation	2012-05-24 10:57:02 -04:00
VariantContextUnitTest.java	New annotation for indels that describe if they're STR's and their characteristics. If an indel is a STR, 3 fields are added to INFO: STR (boolean), RU = repeat unit (String), RPA = number of repetitions per allele. So, for example, if ATATAT* context gets changed to ATAT and ATATATAT, then RU=AT and RPA=3,2,4. Will be made standard annotation shortly. Added unit tests for new functionality. Pending: refactor VariantContextUtils.isRepeat() to unify code, and fix VariantEval functionality.	2012-05-17 15:28:19 -04:00
VariantContextUtilsUnitTest.java	Modified UnitTests to respect reference padding	2012-04-06 16:27:20 -04:00
VariantJEXLContextUnitTest.java	Killing the final versions of old new VariantContext interface	2011-11-18 21:32:43 -05:00